Genotype
Genotypic data is composed of information on DNA sequence variation at many thousands of loci in the genome, which enables us to estimate the genetic relationships between diverse rice varieties and ancestral populations. It helps us to characterize genetic diversity at the sequence level. And it gives us the ability to look for genetic variation associated with phenotypic traits.
To collect large amounts of genetic information for hundreds of individual rice plants, we are developing an efficient molecular marker-based genotyping platform. We were able to utilize previous work from the OryzaSNP project (REF) to identify single base differences in the DNA sequence of diverse rice varieties. The differences we are tracking are called SNPs or single nucleotide polymorphisms. SNPs and other molecular markers can vary between plants, populations, and species, and thus may be used to characterize different individuals and groups. Thousands of SNPs can be assembled on an array—a platform similar to a computer chip—and used to efficiently assess the genetic diversity of an individual rice plant.
Genotyping work with the wild relatives of rice has also been supplemented with data from SSR (Simple Sequence Repeat) markers. These are rapidly-evolving, repeated segments of DNA, useful for assessing genetic similarities and differences among populations and individuals. SSRs were initially used to genotype the O. rufipogon lines to determine genetic relationships among the 100 diverse wild accessions and to select donors for constructing CSSLs (Chromosome Segment Substitution Lines. The genotyping team responsible for the SSR evaluation of O. rufipogon and for developing the SNP arrays is based at Cornell.